Forensic Science International-Genetics最新文献

{"title":"Predicting probative levels of touch DNA on tapelifts using Diamond™ Nucleic Acid Dye","authors":"Isla Madden ,&nbsp;Duncan Taylor ,&nbsp;Natasha Mitchell ,&nbsp;Mariya Goray ,&nbsp;Julianne Henry","doi":"10.1016/j.fsigen.2024.103024","DOIUrl":"10.1016/j.fsigen.2024.103024","url":null,"abstract":"<div><p>Tapelifting is a common strategy to recover touch DNA deposits from porous exhibits in forensic DNA casework. However, it is known that only about 30 % of tapelifts submitted for DNA analysis in operational forensic laboratories yield profiles suitable for comparison or upload to a searchable database. A reliable means to identify and remove non-probative tapelifts from the workflow would reduce sample backlogs and provide significant cost savings. We investigated whether the amount of macroscopic or microscopic fluorescence on a tapelift following staining with Diamond Nucleic Acid Dye (DD), determined using a Polilight and Dino Lite microscope respectively, could predict the DNA yield and/or the DNA profiling outcome using controlled (saliva), semi-controlled (finger mark) and uncontrolled (clothing) samples. Both macroscopic and microscopic DD fluorescence could predict DNA yield and profiling outcome for all sample types, however the predictive power deteriorated as the samples became less controlled. For tapelifts of clothing, which are operationally relevant, Polilight fluorescence scores were significantly impacted by clothing fibres and other non-cellular debris and could not be used to identify non-probative samples. The presence of less than 500 cells on a clothing tapelift using microscopic counting of stained corneocytes was identified as a potential threshold for a non-probative DNA profiling outcome. A broader examination of the reliability of this threshold using a casework trial is recommended. Due to the labour intensiveness of microscopic cell counting, and the increased risk of inadvertent contamination, automation of this process using image software in conjunction with artificial neural networks (ANN) should be explored.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139680200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sunda pangolin (M. javanica) detected for the first time in the Illegal wildlife seizures from northeast India","authors":"Lenrik Konchok Wangmo,&nbsp;Avijit Ghosh,&nbsp;Vinaya Kumar Singh,&nbsp;Stanzin Dolker,&nbsp;Dhriti Banerjee,&nbsp;Lalit Kumar Sharma,&nbsp;Mukesh Thakur","doi":"10.1016/j.fsigen.2024.103023","DOIUrl":"10.1016/j.fsigen.2024.103023","url":null,"abstract":"","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139666206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trace DNA and its persistence on various surfaces: A long term study investigating the influence of surface type and environmental conditions – Part one, metals","authors":"Hilary Arsenault,&nbsp;Agnieszka Kuffel,&nbsp;Niamh Nic Daeid,&nbsp;Alexander Gray","doi":"10.1016/j.fsigen.2024.103011","DOIUrl":"10.1016/j.fsigen.2024.103011","url":null,"abstract":"<div><p>It is imperative for proper evidence triage that forensic biologists understand what kind of results to expect from certain evidence types submitted for DNA analysis. The persistence of trace DNA has been insufficiently investigated and there is little data available pertaining to the persistence of DNA in different environmental conditions and on different materials. The goal of this study is to increase the available data on this topic which would, in turn, help forensic biologists manage expectations when submitting specific evidence types for DNA testing.</p><p>The work presented herein is a large-scale persistence project aimed to identify trends in the persistence of trace DNA and indicate how different environmental storage conditions and target surface characteristics influence the persistence of cellular and cell free DNA (cfDNA) over time. To eliminate variation within the experiment we used a proxy DNA deposit consisting of a synthetic fingerprint solution, cellular DNA, and/or cfDNA. Samples were collected and analysed from 7 metals over the course of 1 year (27 time points) under 3 different environmental storage conditions.</p><p>The results of this experiment show that metal type greatly influences DNA persistence. For instance, copper exhibited an expected poor DNA persistence (up to 4 h) which a purification step did not help increase the DNA yield. Alternatively, DNA can persist for up to a year on lead at levels potentially high enough to allow for forensic DNA testing. Additionally, this study showed that the sample storage environment had no impact on DNA persistence in most cases. When considering DNA type, cfDNA was shown to persist for longer than cellular DNA and persistence as a whole appears to be better when DNA is deposited as mixtures over when deposited alone. Unsurprisingly, it can be expected that DNA recovery rates from trace deposits will decrease over time. However, DNA decay is highly dependent on the metal surface and extremely variable at short time points but slightly less variable as time since deposition increases. This data is intended to add to our understanding of DNA persistence and the factors which affect it.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S187249732400005X/pdfft?md5=9c21cb8f7f17591a9ad53acecfe011c5&pid=1-s2.0-S187249732400005X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139578520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigative use of human environmental DNA in forensic genetics","authors":"Chiara Fantinato ,&nbsp;Peter Gill ,&nbsp;Ane Elida Fonneløp","doi":"10.1016/j.fsigen.2024.103021","DOIUrl":"10.1016/j.fsigen.2024.103021","url":null,"abstract":"<div><p>Individuals leave behind traces of their DNA wherever they go. DNA can be transferred to surfaces and items upon touch, can be released into the air, and may be deposited in indoor dust. The mere presence of individuals in a location is sufficient to facilitate either direct or indirect DNA transfer into the surrounding environment. In this study, we analyzed samples recovered from commonly touched surfaces such as light switches and door handles in an office environment. We evaluated two different methods to isolate DNA and co-extract DNA and RNA from the samples. DNA profiles were compared to the references of the inhabitants of the different locations and were analyzed taking into consideration the type of sampled surface, sampling location and information about the activities in a room during the sampling day. Results from DNA samples collected from surfaces were also compared to those from air and dust samples collected in parallel from the same areas. We characterized the amount and composition of DNA found on various surfaces and showed that surface DNA sampling can be used to detect occupants of a location. The results also indicate that combining information from environmental samples collected from different DNA sources can improve our understanding of DNA transfer events in an indoor setting. This study further demonstrates the potential of human environmental DNA as an investigative tool in forensic genetics.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324000152/pdfft?md5=446e607639d6b121c6597991d42877ac&pid=1-s2.0-S1872497324000152-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139644968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inference of tobacco and alcohol consumption habits from DNA methylation analysis of blood","authors":"A. Ambroa-Conde ,&nbsp;M.A. Casares de Cal ,&nbsp;A. Gómez-Tato ,&nbsp;O. Robinson ,&nbsp;A. Mosquera-Miguel ,&nbsp;M. de la Puente ,&nbsp;J. Ruiz-Ramírez ,&nbsp;C. Phillips ,&nbsp;M.V. Lareu ,&nbsp;A. Freire-Aradas","doi":"10.1016/j.fsigen.2024.103022","DOIUrl":"10.1016/j.fsigen.2024.103022","url":null,"abstract":"<div><p>DNA methylation has become a biomarker of great interest in the forensic and clinical fields. In criminal investigations, the study of this epigenetic marker has allowed the development of DNA intelligence tools providing information that can be useful for investigators, such as age prediction. Following a similar trend, when the origin of a sample in a criminal scenario is unknown, the inference of an individual’s lifestyle such as tobacco use and alcohol consumption could provide relevant information to help in the identification of DNA donors at the crime scene. At the same time, in the clinical domain, prediction of these trends of consumption could allow the identification of people at risk or better identification of the causes of different pathologies. In the present study, DNA methylation data from the UK AIRWAVE study was used to build two binomial logistic models for the inference of smoking and drinking status. A total of 348 individuals (116 non-smokers, 116 former smokers and 116 smokers) plus a total of 237 individuals (79 non-drinkers, 79 moderate drinkers and 79 drinkers) were used for development of tobacco and alcohol consumption prediction models, respectively. The tobacco prediction model was composed of two CpGs (cg05575921 in <em>AHRR</em> and cg01940273) and the alcohol prediction model three CpGs (cg06690548 in <em>SLC7A11</em>, cg0886875 and cg21294714 in <em>MIR4435–2HG</em>), providing correct classifications of 86.49% and 74.26%, respectively. Validation of the models was performed using leave-one-out cross-validation. Additionally, two independent testing sets were also assessed for tobacco and alcohol consumption. Considering that the consumption of these substances could underlie accelerated epigenetic ageing patterns, the effect of these lifestyles on the prediction of age was evaluated. To do that, a quantile regression model based on previous studies was generated, and the potential effect of tobacco and alcohol consumption with the epigenetic age was assessed. The Wilcoxon test was used to evaluate the residuals generated by the model and no significant differences were observed between the categories analyzed.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324000164/pdfft?md5=557b64fb62b0f20c161ac6e8e8286a69&pid=1-s2.0-S1872497324000164-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139578391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Title page","authors":"","doi":"10.1016/S1872-4973(24)00009-7","DOIUrl":"https://doi.org/10.1016/S1872-4973(24)00009-7","url":null,"abstract":"","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324000097/pdfft?md5=02ea06511b4874b73433c906907d85cc&pid=1-s2.0-S1872497324000097-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139653487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Response of salivary microbiome to temporal, environmental, and surface characteristics under in vitro exposure","authors":"Litao Huang ,&nbsp;Xiaomin Liang ,&nbsp;Guichao Xiao ,&nbsp;Jieyu Du ,&nbsp;Linying Ye ,&nbsp;Qin Su ,&nbsp;Chao Liu ,&nbsp;Ling Chen","doi":"10.1016/j.fsigen.2024.103020","DOIUrl":"10.1016/j.fsigen.2024.103020","url":null,"abstract":"<div><p><span><span>The microbiome of saliva stains deposited at crime scenes and in everyday settings is valuable for forensic investigations and environmental ecology. However, the dynamics and applications of microbial communities in these saliva stains have not been fully explored. In this study, we analyzed saliva samples that were exposed to indoor conditions for up to 1 year and to different carriers (cotton, sterile absorbent cotton swab, woolen, dacron) in both indoor and </span>outdoor environments for 1 month using high-throughput sequencing. The analysis of microbial composition and Mfuzz clustering showed that the salivary flora, specifically </span><span><em>Streptococcus</em></span> (cluster7), which was associated with microbial contamination, remained stable over short periods of time. However, prolonged exposure led to significant differences due to the invasion of environmental bacteria such as <span><em>Pseudomonas</em></span> and <span><em>Achromobacter</em></span><span>. The growth and colonization of environmental flora were promoted by humidity. The neutral model predictions indicated that the assembly of salivary microbial communities in outdoor environments was significantly influenced by stochastic processes, with environmental characteristics having a greater impact on community change compared to surface characteristics. By incorporating data from previous studies on fecal and vaginal secretion microbiology, we developed RF and XGBoost classification models that achieved high accuracy (&gt;98 %) and AUC (&gt;0.8). Additionally, a RF regression model was created to determine the time since deposition (TsD) of the stains. Time inference models yielded a mean absolute error (MAE) of 7.1 days for stains exposed for 1 year and 14.2 h for stains exposed for 14 days. These findings enhance our understanding of the changes in the microbiome of saliva stains over time, in different environments, and on different surfaces. They also have potential applications in assessing potential microbial contamination, identifying body fluids, and inferring the time of deposition.</span></p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139553156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Harmonizing the forensic nomenclature for STR loci D6S474 and DYS612","authors":"Martin Bodner ,&nbsp;David Ballard ,&nbsp;Lisa A. Borsuk ,&nbsp;Jonathan L. King ,&nbsp;Walther Parson ,&nbsp;Christopher Phillips ,&nbsp;Katherine Butler Gettings","doi":"10.1016/j.fsigen.2024.103012","DOIUrl":"10.1016/j.fsigen.2024.103012","url":null,"abstract":"<div><p>The autosomal STR D6S474 and the Y-chromosomal STR DYS612 have been reported in multiple ways in the forensic literature, with differences in both the bracketed repeat structures and counting of numerical length-based capillary electrophoresis (CE) alleles. These issues often come to light when STR loci are introduced in commercial assays and results compared with historical publications of allele frequency data, or multiple assays are characterized with reference materials. We review the forensic literature and other relevant information, and provide suggestions for the future treatment of each STR.</p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1872497324000061/pdfft?md5=044f41518cd7faa1d92df7289b7ca5a8&pid=1-s2.0-S1872497324000061-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139539625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive landscape of non-CODIS STRs in global populations provides new insights into challenging DNA profiles","authors":"Yuguo Huang ,&nbsp;Mengge Wang ,&nbsp;Chao Liu ,&nbsp;Guanglin He","doi":"10.1016/j.fsigen.2024.103010","DOIUrl":"10.1016/j.fsigen.2024.103010","url":null,"abstract":"<div><p><span>The worldwide implementation of short tandem repeats<span><span><span> (STR) profiles in forensic genetics necessitated establishing and expanding the </span>CODIS core loci set to facilitated efficient data management and exchange. Currently, the mainstay CODIS STRs are adopted in most general-purpose forensic kits. However, relying solely on these loci failed to yield satisfactory results for challenging tasks, such as bio-geographical </span>ancestry inference, complex DNA mixture profile interpretation, and distant kinship analysis. In this context, non-CODIS STRs are potent supplements to enhance the systematic discriminating power, particularly when combined with the high-throughput next-generation sequencing (NGS) technique. Nevertheless, comprehensive evaluation on non-CODIS STRs in diverse populations was scarce, hindering their further application in routine caseworks. To address this gap, we investigated genetic variations of 178 historically available non-CODIS STRs from ethnolinguistically different worldwide populations and studied their characteristics and forensic potentials via high-coverage </span></span>whole genome sequencing<span> (WGS) data. Initially, we delineated the genomic properties of these non-CODIS markers through sequence searching, repeat structure scanning, and manual inspection. Subsequent population genetics<span> analysis suggested that these non-CODIS STRs had comparable polymorphism levels and forensic utility to CODIS STRs. Furthermore, we constructed a theoretical next-generation sequencing (NGS) panel comprising 108 STRs (20 CODIS STRs and 88 non-CODIS STRs), and evaluated its performance in inferring bio-geographical ancestry origins, deconvoluting complex DNA mixtures, and differentiating distant kinships using real and simulated datasets. Our findings demonstrated that incorporating supplementary non-CODIS STRs enabled the extrapolation of multidimensional information from a single STR profile, thereby facilitating the analysis of challenging forensic tasks. In conclusion, this study presents an extensive genomic landscape of forensic non-CODIS STRs among global populations, and emphasized the imperative inclusion of additional polymorphic non-CODIS STRs in future NGS-based forensic systems.</span></span></p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139507364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequence-based population structure, relatedness, and inbreeding estimates for forensic autosomal STR markers","authors":"Sanne E. Aalbers ,&nbsp;Bruce S. Weir","doi":"10.1016/j.fsigen.2024.103009","DOIUrl":"10.1016/j.fsigen.2024.103009","url":null,"abstract":"<div><p><span>Population data have become available for sequence data to aid forensic investigations and prepare the forensic community in the move towards implementing NGS methods. This comes with a need for updated population genetic parameters estimates to allow </span>DNA<span> evidence evaluations using sequence data. Initial work has been done on a small sample and here we expand this work by providing estimates of population structure and relatedness for autosomal STR data generated by sequencing technologies. We also discuss the effect of inbreeding on forensic calculations and discuss why the use of genotypic-based estimates may be preferred over allelic-based estimates.</span></p></div>","PeriodicalId":50435,"journal":{"name":"Forensic Science International-Genetics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139470606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}